ARIES: Autonomous Reasoning with LLMs on Interactive Thought Graph Environments

Recent research has shown that LLM performance on reasoning tasks can be enhanced by scaling test-time compute. One promising approach, particularly with decomposable problems, involves arranging intermediate solutions as a graph on which transformations are performed to explore the solution space. However, prior works rely on pre-determined, task-specific transformation schedules which are subject to a set of searched hyperparameters. In this work, we view thought graph transformations as actions in a Markov decision process, and implement policy agents to drive effective action policies for the underlying reasoning LLM agent. In particular, we investigate the ability for another LLM to act as a policy agent on thought graph environments and introduce ARIES, a multi-agent architecture for reasoning with LLMs. In ARIES, reasoning LLM agents solve decomposed subproblems, while policy LLM agents maintain visibility of the thought graph states, and dynamically adapt the problem-solving strategy. Through extensive experiments, we observe that using off-the-shelf LLMs as policy agents with no supervised fine-tuning (SFT) can yield up to $29\%$ higher accuracy on HumanEval relative to static transformation schedules, as well as reducing inference costs by $35\%$ and avoid any search requirements. We also conduct a thorough analysis of observed failure modes, highlighting that limitations on LLM sizes and the depth of problem decomposition can be seen as challenges to scaling LLM-guided reasoning.

AMPLE: Event-Driven Accelerator for Mixed-Precision Inference of Graph Neural Networks

Graph Neural Networks (GNNs) have recently gained attention due to their performance on non-Euclidean data. The use of custom hardware architectures proves particularly beneficial for GNNs due to their irregular memory access patterns, resulting from the sparse structure of graphs. However, existing FPGA accelerators are limited by their double buffering mechanism, which doesn't account for the irregular node distribution in typical graph datasets. To address this, we introduce \textbf{AMPLE} (Accelerated Message Passing Logic Engine), an FPGA accelerator leveraging a new event-driven programming flow. We develop a mixed-arithmetic architecture, enabling GNN inference to be quantized at a node-level granularity. Finally, prefetcher for data and instructions is implemented to optimize off-chip memory access and maximize node parallelism. Evaluation on citation and social media graph datasets ranging from $2$K to $700$K nodes showed a mean speedup of $243\times$ and $7.2\times$ against CPU and GPU counterparts, respectively.

Cached Multi-Lora Composition for Multi-Concept Image Generation

Low-Rank Adaptation (LoRA) has emerged as a widely adopted technique in text-to-image models, enabling precise rendering of multiple distinct elements, such as characters and styles, in multi-concept image generation. However, current approaches face significant challenges when composing these LoRAs for multi-concept image generation, resulting in diminished generated image quality. In this paper, we initially investigate the role of LoRAs in the denoising process through the lens of the Fourier frequency domain. Based on the hypothesis that applying multiple LoRAs could lead to "semantic conflicts", we find that certain LoRAs amplify high-frequency features such as edges and textures, whereas others mainly focus on low-frequency elements, including the overall structure and smooth color gradients. Building on these insights, we devise a frequency domain based sequencing strategy to determine the optimal order in which LoRAs should be integrated during inference. This strategy offers a methodical and generalizable solution compared to the naive integration commonly found in existing LoRA fusion techniques. To fully leverage our proposed LoRA order sequence determination method in multi-LoRA composition tasks, we introduce a novel, training-free framework, Cached Multi-LoRA (CMLoRA), designed to efficiently integrate multiple LoRAs while maintaining cohesive image generation. With its flexible backbone for multi-LoRA fusion and a non-uniform caching strategy tailored to individual LoRAs, CMLoRA has the potential to reduce semantic conflicts in LoRA composition and improve computational efficiency. Our experimental evaluations demonstrate that CMLoRA outperforms state-of-the-art training-free LoRA fusion methods by a significant margin -- it achieves an average improvement of $2.19\%$ in CLIPScore, and $11.25\%$ in MLLM win rate compared to LoraHub, LoRA Composite, and LoRA Switch.

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

Refining Salience-Aware Sparse Fine-Tuning Strategies for Language Models

Parameter-Efficient Fine-Tuning (PEFT) has gained prominence through low-rank adaptation methods like LoRA. In this paper, we focus on sparsity-based PEFT (SPEFT), which introduces trainable sparse adaptations to the weight matrices in the model, offering greater flexibility in selecting fine-tuned parameters compared to low-rank methods. We conduct the first systematic evaluation of salience metrics for SPEFT, inspired by zero-cost NAS proxies, and identify simple gradient-based metrics is reliable, and results are on par with the best alternatives, offering both computational efficiency and robust performance. Additionally, we compare static and dynamic masking strategies, finding that static masking, which predetermines non-zero entries before training, delivers efficiency without sacrificing performance, while dynamic masking offers no substantial benefits. Across NLP tasks, a simple gradient-based, static SPEFT consistently outperforms other fine-tuning methods for LLMs, providing a simple yet effective baseline for SPEFT. Our work challenges the notion that complexity is necessary for effective PEFT. Our work is open source and available to the community at [https://github.com/0-ml/speft].

Hardware and Software Platform Inference

It is now a common business practice to buy access to large language model (LLM) inference rather than self-host, because of significant upfront hardware infrastructure and energy costs. However, as a buyer, there is no mechanism to verify the authenticity of the advertised service including the serving hardware platform, e.g. that it is actually being served using an NVIDIA H100. Furthermore, there are reports suggesting that model providers may deliver models that differ slightly from the advertised ones, often to make them run on less expensive hardware. That way, a client pays premium for a capable model access on more expensive hardware, yet ends up being served by a (potentially less capable) cheaper model on cheaper hardware. In this paper we introduce \textit{\textbf{hardware and software platform inference (HSPI)}} -- a method for identifying the underlying \GPU{} architecture and software stack of a (black-box) machine learning model solely based on its input-output behavior. Our method leverages the inherent differences of various \GPU{} architectures and compilers to distinguish between different \GPU{} types and software stacks. By analyzing the numerical patterns in the model's outputs, we propose a classification framework capable of accurately identifying the \GPU{} used for model inference as well as the underlying software configuration. Our findings demonstrate the feasibility of inferring \GPU{} type from black-box models. We evaluate HSPI against models served on different real hardware and find that in a white-box setting we can distinguish between different \GPU{}s with between $83.9\%$ and $100\%$ accuracy. Even in a black-box setting we are able to achieve results that are up to three times higher than random guess accuracy.

Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences

Abstract Recent advances in immunology and synthetic biology have accelerated the development of deep generative methods for DNA sequence design. Two dominant approaches in this field are AutoRegressive (AR) models and Diffusion Models (DMs). However, genomic sequences are functionally heterogeneous, consisting of multiple connected regions (e.g., Promoter Regions, Exons, and Introns) where elements within each region come from the same probability distribution, but the overall sequence is non-homogeneous. This heterogeneous nature presents challenges for a single model to accurately generate genomic sequences. In this paper, we analyze the properties of AR models and DMs in heterogeneous genomic sequence generation, pointing out crucial limitations in both methods: (i) AR models capture the underlying distribution of data by factorizing and learning the transition probability but fail to capture the global property of DNA sequences. (ii) DMs learn to recover the global distribution but tend to produce errors at the base pair level. To overcome the limitations of both approaches, we propose a post-training sampling method, termed Absorb & Escape (A&E) to perform compositional generation from AR models and DMs. This approach starts with samples generated by DMs and refines the sample quality using an AR model through the alternation of the Absorb and Escape steps. To assess the quality of generated sequences, we conduct extensive experiments on 15 species for conditional and unconditional DNA generation. The experiment results from motif distribution, diversity checks, and genome integration tests unequivocally show that A&E outperforms state-of-the-art AR models and DMs in genomic sequence generation.

Scaling Laws for Mixed quantization in Large Language Models

Post-training quantization of Large Language Models (LLMs) has proven effective in reducing the computational requirements for running inference on these models. In this study, we focus on a straightforward question: When aiming for a specific accuracy or perplexity target for low-precision quantization, how many high-precision numbers or calculations are required to preserve as we scale LLMs to larger sizes? We first introduce a critical metric named the quantization ratio, which compares the number of parameters quantized to low-precision arithmetic against the total parameter count. Through extensive and carefully controlled experiments across different model families, arithmetic types, and quantization granularities (e.g. layer-wise, matmul-wise), we identify two central phenomenons. 1) The larger the models, the better they can preserve performance with an increased quantization ratio, as measured by perplexity in pre-training tasks or accuracy in downstream tasks. 2) The finer the granularity of mixed-precision quantization (e.g., matmul-wise), the more the model can increase the quantization ratio. We believe these observed phenomena offer valuable insights for future AI hardware design and the development of advanced Efficient AI algorithms.

QERA: an Analytical Framework for Quantization Error Reconstruction

he growing number of parameters and computational demands of large language models (LLMs) present significant challenges for their efficient deployment. Recently, there is an increasing interest in quantizing weights to extremely low precision while offsetting the resulting error with low-rank, high-precision error reconstruction terms. The combination of quantization and low-rank approximation is now popular in both adapter-based, parameter-efficient fine-tuning methods such as LoftQ and low-precision inference techniques including ZeroQuant-V2. Usually, the low-rank terms are calculated via the singular value decomposition (SVD) of the weight quantization error, minimizing the Frobenius and spectral norms of the weight approximation error. Recent methods like LQ-LoRA and LQER introduced hand-crafted heuristics to minimize errors in layer outputs (activations) rather than weights, resulting improved quantization results. However, these heuristic methods lack an analytical solution to guide the design of quantization error reconstruction terms. In this paper, we revisit this problem and formulate an analytical framework, named Quantization Error Reconstruction Analysis (QERA), and offer a closed-form solution to the problem. We show QERA benefits both existing low-precision fine-tuning and inference methods -- QERA achieves a fine-tuned accuracy gain of $\Delta_{\text{acc}}$ = 6.05% of 2-bit RoBERTa-base on GLUE compared to LoftQ; and obtains $\Delta_{\text{acc}}$ = 2.97% higher post-training quantization accuracy of 4-bit Llama-3.1-70B on average than ZeroQuant-V2 and $\Delta_{\text{ppl}}$ = - 0.28 lower perplexity on WikiText2 than LQER.

GV-Rep: A Large-Scale Dataset for Genetic Variant Representation Learning

Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential increase in patient-level GV data. This growth poses a challenge for clinicians who must efficiently prioritize patient-specific GVs and integrate them with existing genomic databases to inform patient management. To addressing the interpretation of GVs, genomic foundation models (GFMs) have emerged. However, these models lack standardized performance assessments, leading to considerable variability in model evaluations. This poses the question: How effectively do deep learning methods classify unknown GVs and align them with clinically-verified GVs? We argue that representation learning, which transforms raw data into meaningful feature spaces, is an effective approach for addressing both indexing and classification challenges. We introduce a large-scale Genetic Variant dataset, named GV-Rep, featuring variable-length contexts and detailed annotations, designed for deep learning models to learn GV representations across various traits, diseases, tissue types, and experimental contexts. Our contributions are three-fold: (i) Construction of a comprehensive dataset with 7 million records, each labeled with characteristics of the corresponding variants, alongside additional data from 17,548 gene knockout tests across 1,107 cell types, 1,808 variant combinations, and 156 unique clinically verified GVs from real-world patients. (ii) Analysis of the structure and properties of the dataset. (iii) Experimentation of the dataset with pre-trained GFMs. The results show a significant gap between GFMs current capabilities and accurate GV representation. We hope this dataset will help advance genomic deep learning to bridge this gap.